problems about converting cp2k results to datasets by using cp2kdata

[dlProjectYue]

When I use cp2kdata to convert the cp2k results, I get the wrong results:

I don't know how to fix this. Please help me!

[robinzyb]

could you please provide the script?

[dlProjectYue]

And another problem is that, when I tried to run 1step MD by excluding above script and use dpdata. It shows wrong information bellow:

I searched about similar solution which you said that I should delete the energy file. But actually I don't know why this happened. I run 1 step MD, but energy file shows two results. which line in scripts caused this? Could you please help me?

[dlProjectYue]

When I used this md.inp, it still shows AssertionError, assert first_cell.shape==(1,3,3). I don't know why.
md (2).zip

[dlProjectYue]

And another problem is that, when I tried to run 1step MD by excluding above script and use dpdata. It shows wrong information bellow: I searched about similar solution which you said that I should delete the energy file. But actually I don't know why this happened. I run 1 step MD, but energy file shows two results. which line in scripts caused this? Could you please help me?

I know that this is due to the output frequency. If I set printing frequency of different parameters as 1, it didn't show this information.

[robinzyb]

could you please provide the script?

The python code you used to covert cp2k data

[dlProjectYue]

I just use codes like "data=dpdata.LabeledSystem('./',cp2k_output_name='output_file.log',fmt='cp2kdata/md')"

[robinzyb]

There are some errors on parsing the output. I would like to request you to upload the output in order to diagnise.

[robinzyb]

cp2k_output_name=None

[dlProjectYue]

Thanks for your suggestion! I tried to use data=dpdata.LabeledSystem(cp2k_output_name=None) , it shows no error. But data actually has 0 frame.

[robinzyb]

supposed to be the following,

cells = np.arrary([[10.0, 0, 0], [0,10,0], [0,0,10]])
data=dpdata.LabeledSystem('./',cp2k_output_name=None, cells=cells, fmt='cp2kdata/md')

because the cells information is expected to be provided by users instead of output
anyhow, glad to see you solve the problem.

One last thing, once everything's sorted, could you mark one reply as the answer and close this discussion? Thank you and have a good day.

[dlProjectYue]

Sorry to bother you again. Even though I know the results, I tried to use your suggestion but it shows the errors like this.

[robinzyb]

this means the cp2kdata and dpdata are not installed under same environment

[qizh5]

Sorry, I met the same question with [dlProjectYue], and I try to delete output.out file .
And the python code is
cells = np.array([[16.0, 0, 0], [0,16,0], [0,0,16]])
data=dpdata.LabeledSystem('./',cp2k_output_name=None, cells=cells, fmt='cp2kdata/md')
It gave the following error message.

It seems that an output file must be provided. I don't konw what the problem is. Could you help me?

[qizh5]

It's my output file
Uploading output.zip…

[robinzyb]

This is a bug. It is caused by the repetitive information from

 CELL_TOP| Volume [angstrom^3]:                                         4096.000
 CELL_TOP| Vector a [angstrom    16.000     0.000     0.000    |a| =      16.000
 CELL_TOP| Vector b [angstrom     0.000    16.000     0.000    |b| =      16.000
 CELL_TOP| Vector c [angstrom     0.000     0.000    16.000    |c| =      16.000
 CELL_TOP| Angle (b,c), alpha [degree]:                                   90.000
 CELL_TOP| Angle (a,c), beta  [degree]:                                   90.000
 CELL_TOP| Angle (a,b), gamma [degree]:                                   90.000
 CELL_TOP| Numerically orthorhombic:                                         YES
 
 GENERATE|  Preliminary Number of Bonds generated:                             0
 GENERATE|  Achieved consistency in connectivity generation.

 CELL| Volume [angstrom^3]:                                             4096.000
 CELL| Vector a [angstrom]:      16.000     0.000     0.000    |a| =      16.000
 CELL| Vector b [angstrom]:       0.000    16.000     0.000    |b| =      16.000
 CELL| Vector c [angstrom]:       0.000     0.000    16.000    |c| =      16.000
 CELL| Angle (b,c), alpha [degree]:                                       90.000
 CELL| Angle (a,c), beta  [degree]:                                       90.000
 CELL| Angle (a,b), gamma [degree]:                                       90.000
 CELL| Numerically orthorhombic:                                             YES

 CELL_REF| Volume [angstrom^3]:                                         4096.000
 CELL_REF| Vector a [angstrom    16.000     0.000     0.000    |a| =      16.000
 CELL_REF| Vector b [angstrom     0.000    16.000     0.000    |b| =      16.000
 CELL_REF| Vector c [angstrom     0.000     0.000    16.000    |c| =      16.000
 CELL_REF| Angle (b,c), alpha [degree]:                                   90.000
 CELL_REF| Angle (a,c), beta  [degree]:                                   90.000
 CELL_REF| Angle (a,b), gamma [degree]:                                   90.000
 CELL_REF| Numerically orthorhombic:                                         YES

in output.

The quick way to resolve the problem is deleting extra CELL infomation in the output and keeping only one cell infomation. You could try this first.
I will fix the bug later on.

[qizh5]

Excuse me, may I ask for detailed information on which part to delete, cell_top,cell,or cell_ref? It should be okay,if i only keep the following part? CELL_TOP| Volume [angstrom^3]: 4096.000 CELL_TOP| Vector a [angstrom 16.000 0.000 0.000 |a| = 16.000 CELL_TOP| Vector b [angstrom 0.000 16.000 0.000 |b| = 16.000 CELL_TOP| Vector c [angstrom 0.000 0.000 16.000 |c| = 16.000 CELL_TOP| Angle (b,c), alpha [degree]: 90.000 CELL_TOP| Angle (a,c), beta [degree]: 90.000 CELL_TOP| Angle (a,b), gamma [degree]: 90.000 CELL_TOP| Numerically orthorhombic: YES

GENERATE| Preliminary Number of Bonds generated: 0 GENERATE| Achieved consistency in connectivity generation.

Excuse me, may I ask for detailed information on which part to delete, cell_top,cell,or cell_ref?
It should be okay,if i only keep the following part?
CELL_TOP| Volume [angstrom^3]: 4096.000
CELL_TOP| Vector a [angstrom 16.000 0.000 0.000 |a| = 16.000
CELL_TOP| Vector b [angstrom 0.000 16.000 0.000 |b| = 16.000
CELL_TOP| Vector c [angstrom 0.000 0.000 16.000 |c| = 16.000
CELL_TOP| Angle (b,c), alpha [degree]: 90.000
CELL_TOP| Angle (a,c), beta [degree]: 90.000
CELL_TOP| Angle (a,b), gamma [degree]: 90.000
CELL_TOP| Numerically orthorhombic: YES

GENERATE| Preliminary Number of Bonds generated: 0
GENERATE| Achieved consistency in connectivity generation.

[robinzyb]

You will find the part I quote is repetitive in the output. Just keep one of them.

[qizh5]

You will find the part I quote is repetitive in the output. Just keep one of them.

Got it!!!!Thanks for your teaching ,now it works well!!!!!

[robinzyb]

glad you have solve it!